GAGE: A critical evaluation of genome assemblies and assembly algorithms.

By Steven L. Salzberg, Adam M. Phillippy, Aleksey V. Zimin, Daniela Puiu, Tanja Magoc, Sergey Koren, Todd J. Treangen, Michael C. Schatz, Arthur L. Delcher, Michael Roberts and 3 more. Genome Research, 2012

354 citations recorded by the source corpus.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/8ec44ba4a4c13b8108d00785ea31446d5becd87a

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Citations in the corpus

An Integrated Pipeline for de Novo Assembly of Microbial Genomes (2012, methodology): “Broad performance comparisons of many assemblers on many datasets is a major undertaking and we hope that A5 can be included in future comparisons like GAGE and the Assemblathon [14,15].”
Big Data Application in Biomedical Research and Health Care: A Literature Review (2016, methodology): “41 The CloudRS team evaluated the system on six different datasets using the GAGE benchmarks, 42 and the results show that CloudRS has a higher precision rate compared with the Reptile 43 method.”
MeDuSa: a multi-draft based scaffolder (2015, methodology): “Two of them were retrieved from the SRA archive database (ECOL, RSPH), the SAUR dataset was obtained from the GAGE benchmark study (Salzberg et al., 2012) whereas the BCEN and MTUB datasets were obtained from in house performed Illumina HiSeq sequencing runs with a fragment size of 500bp.”
Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage (2015, positive): “One concern generated by the pre-polished assemblies was that their N50s were high, but their corrected N50s (23) after accounting for errors were low; however, Quiver and Pilon polishing dramatically improved the corrected N50s of the assemblies, indicating that the low corrected N50 values were du”
Toward almost closed genomes with GapFiller (2012, methodology): “Random paired-end reads were created using wgsim (at default settings), which is part of the SAM tools package [12].”
The Genome 10K Project: A Way Forward (2015, neutral): “Armadillos (21, 1) Sloths (6, 1) Anteaters (4, 0) Elephant shrews (15, 1) Tenrecs, golden moles (51, 2) Aardvark (1, 1) Elephants (3, 1) Hyraxes (4, 1) Dugong, manatees (5, 1) Shrews, moles, hedgehogs (452, 3) Even-toed ungulates, cetaceans (324, 25) Bats (1116, 11) Odd-toed ungulates (17, 3) Pangol”
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler (2012, background): “detect and revise these sequencing errors in reads before assembly [2,7].”
Circlator: automated circularization of genome assemblies using long sequencing reads (2015, methodology): “3 with the options --gage -R to use a reference sequence and run the GAGE [17] analysis.”
Space-efficient and exact de Bruijn graph representation based on a Bloom filter (2012, neutral): “The Illumina dataset is from the GAGE benchmark [21] (100 bp reads, all short paired-end libraries).”
GapFiller: a de novo assembly approach to fill the gap within paired reads (2012, methodology): “We produced a set of statistics representing the correctness of our assembly using the same scripts used in [9] and available for download at [28].”
Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes (2014, methodology): “For each COG the MGS assembly and reference proteins were aligned using muscle and here joined to a single alignment file for each COG using muscle - profile .”